EMBOSS: Project Meeting (Mon 15th Aug 11)
1. Minutes of the last meeting
Minutes of the meeting of 8th August 2011 are
2. Maintenance etc.
Peter has added reference sequence and assembly applications,
called refseqget and assemblyget, plus an
application variationget for variation data.
Peter has installed mira release 3.4rc3 for
testing. >b>Mahmut is testing assembly formats in mira 3.2.
Peter has extended the query language syntax to allow more
flexible ways to append a sequence range. Both ":start:end" and
":start..end" are allowed each with a ":r" suffix to
reverse the range.
Peter has renamed QA tests to provide a "keep" or "ex" suffix
but not both.
3. New developments
3.1 Reference sequences
Peter has written a parser for CON (contig) entries in EMBL
which picks up the individual sequence regions and builds a complete
sequence. Some CON entries in EMBL were found to refer to renamed
entries. The ENA support desk has been notified. The entries are owned
by the submitters, so they have been asked to update the CON entries
to match the renamed whole genome shotgun (WGS) fragments.
Peter will consider qualifier names to control the resolution
of reference sequence and assembly inputs (reading the sequence only
if resolution is to the level of individual bases).
The AjPRefseq data object includes a list of sequence fragments
with position and length so we can later read a specified region
without loading the entire sequence.
Peter has defined a new database attribute "special:"
which can appear multiple times in a database definition. The value is
a "name-value" where the name is specific to the assembly
method. This can include the species ID currently defined as a comment
in 6.4.0 for Ensembl genomes.
Alan has reported releasing the first set of patches to 6.4.0
and a new mEMBOSS build 220.127.116.11.
Peter will ask the SAB for suggestions on a new homepage for
5. Documentation and Training
5.1 Web server
6. User queries and answers
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 22nd August.